New transgenic crops with improved farming, food and feeding traits are progressively being developed. Although the commercialization of transgenic plants started early 1990s, necessity for analysis of unintended effects of the transgenes hampers preparing required documents for their release. Currently, Agrobacterium-mediated plant genetic engineering methods relies on the integration of foreign (often prokaryotic) DNA, such as transgenes, promoters, terminators and T-DNA, into plant genomes. For example, cry3 gene (GenBank Accession AY572010.1), coding for a BT protein, contains 2.7% of CpG motif, a known characteristic of prokaryotic DNA). Some interactions between inserted prokaryotic DNA and plant immune system are documented.